LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693



# Initialize simulation box
dimension       3
boundary        p p p
units           real
atom_style      molecular

# Set potential styles
pair_style      hybrid/overlay table spline 500 local/density

# Read molecule data and set initial velocities
read_data       benzene_water.data
Reading data file ...
  orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
  1 by 1 by 4 MPI processor grid
  reading atoms ...
  1380 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.007 seconds
velocity        all create  3.0000e+02 16611 rot yes dist gaussian

# Assign potentials
pair_coeff          1     1    table          benzene_water.pair.table      PairBB
WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 150 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairBB to re-computed values (src/pair_table.cpp:473)
pair_coeff          1     2    table          benzene_water.pair.table      PairWW
WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 90 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairWW to re-computed values (src/pair_table.cpp:473)
pair_coeff          2     2    table          benzene_water.pair.table      PairBW
WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 135 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairBW to re-computed values (src/pair_table.cpp:473)
pair_coeff          *     *    local/density  benzene_water.localdensity.table

# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box

# Thermostat & time integration
timestep        2.0
thermo          100
thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl

# Minimization
minimize        1.e-4 0.0 10000 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair_style  local/density  command:

@Article{Sanyal16,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
 journal = {J.~Chem.~Phys.},
 year =    2016,
 DOI = doi.org/10.1063/1.4958629}

@Article{Sanyal18,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
 journal = {J.~Phys.~Chem. B},
 year =    2018,
 DOI = doi.org/10.1021/acs.jpcb.7b12446}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 15.25
  ghost atom cutoff = 15.25
  binsize = 7.625, bins = 4 4 18
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair table, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair local/density, perpetual, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 8.441 | 8.589 | 8.688 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
         300    1233.1611    2374.6749     3607.836            0            0            0    2374.6749 
         300    1233.1611    1024.8113    2257.9724            0            0            0    1024.8113 
Loop time of 0.240559 on 4 procs for 74 steps with 1380 atoms

98.5% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
      2374.67491482358   1024.89407898645   1024.81130011575
  Force two-norm initial, final = 263.77519 20.459697
  Force max component initial, final = 22.412654 8.6082349
  Final line search alpha, max atom move = 0.027790997 0.23923143
  Iterations, force evaluations = 74 118

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.15928    | 0.1873     | 0.22814    |   6.5 | 77.86
Bond    | 3.857e-06  | 4.4012e-06 | 5.496e-06  |   0.0 |  0.00
Neigh   | 0.00064142 | 0.0028761  | 0.0058864  |   4.2 |  1.20
Comm    | 0.0040776  | 0.039595   | 0.074187   |  12.6 | 16.46
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.01078    |            |       |  4.48

Nlocal:        345.000 ave         664 max         147 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost:        2850.50 ave        4438 max        1208 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:        19377.5 ave       37718 max        7456 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 77510
Ave neighs/atom = 56.166667
Ave special neighs/atom = 0.0000000
Neighbor list builds = 3
Dangerous builds = 0

# Set up integration parameters
fix             timeintegration all nve
fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890

# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep  0
run             5000
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 7.316 | 7.465 | 7.563 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
         300    1233.1611    1024.8113    2257.9724            0            0            0    1024.8113 
   263.61917    1083.6164     1866.745    2950.3614            0            0            0     1866.745 
    296.0253     1216.823    2122.8463    3339.6692            0            0            0    2122.8463 
   301.93846    1241.1292    2172.9802    3414.1095            0            0            0    2172.9802 
    293.9491    1208.2887    2205.4892    3413.7779            0            0            0    2205.4892 
   286.33795    1177.0027    2204.8908    3381.8935            0            0            0    2204.8908 
   295.48217    1214.5904    2230.8849    3445.4753            0            0            0    2230.8849 
   293.88908    1208.0419    2218.7563    3426.7982            0            0            0    2218.7563 
   295.13798    1213.1756    2277.4515    3490.6271            0            0            0    2277.4515 
   290.39538     1193.681    2273.4385    3467.1195            0            0            0    2273.4385 
   297.56782    1223.1635    2268.7182    3491.8817            0            0            0    2268.7182 
   306.45578    1259.6978    2289.1507    3548.8486            0            0            0    2289.1507 
   308.54582     1268.289    2284.8514    3553.1404            0            0            0    2284.8514 
   302.17353    1242.0955    2262.5577    3504.6532            0            0            0    2262.5577 
   295.30087    1213.8452    2315.8853    3529.7305            0            0            0    2315.8853 
   308.59197    1268.4787    2291.8314    3560.3101            0            0            0    2291.8314 
   297.75618    1223.9378    2287.2003    3511.1381            0            0            0    2287.2003 
   303.43395    1247.2765    2297.7158    3544.9923            0            0            0    2297.7158 
   307.16233    1262.6021    2255.9769    3518.5791            0            0            0    2255.9769 
   301.34428    1238.6868     2284.416    3523.1028            0            0            0     2284.416 
   295.43209    1214.3846    2294.1043    3508.4889            0            0            0    2294.1043 
   287.86904    1183.2963    2257.0204    3440.3168            0            0            0    2257.0204 
    297.2661    1221.9233    2251.4194    3473.3428            0            0            0    2251.4194 
   298.90221    1228.6486     2261.834    3490.4826            0            0            0     2261.834 
   288.07202    1184.1307    2284.1918    3468.3225            0            0            0    2284.1918 
   300.41201    1234.8547    2303.9573     3538.812            0            0            0    2303.9573 
   283.91279     1167.034    2329.7936    3496.8277            0            0            0    2329.7936 
   297.27507    1221.9602    2337.0516    3559.0118            0            0            0    2337.0516 
   296.22263    1217.6341    2335.6424    3553.2765            0            0            0    2335.6424 
   296.13784    1217.2856    2364.7034     3581.989            0            0            0    2364.7034 
   308.17642    1266.7706    2320.2753    3587.0459            0            0            0    2320.2753 
   310.26592    1275.3596    2301.9318    3577.2914            0            0            0    2301.9318 
   292.97391    1204.2801    2289.8116    3494.0917            0            0            0    2289.8116 
   294.81231    1211.8369    2315.0388    3526.8757            0            0            0    2315.0388 
   298.66155    1227.6594    2317.2844    3544.9437            0            0            0    2317.2844 
   302.77939    1244.5859    2301.2063    3545.7922            0            0            0    2301.2063 
   291.47597    1198.1228    2285.1757    3483.2985            0            0            0    2285.1757 
   286.19045    1176.3964    2265.2665    3441.6629            0            0            0    2265.2665 
   295.58144    1214.9984    2272.3165     3487.315            0            0            0    2272.3165 
   283.86988    1166.8577    2320.6142    3487.4719            0            0            0    2320.6142 
    300.0576    1233.3979    2330.8962    3564.2941            0            0            0    2330.8962 
   299.86413    1232.6026    2321.2281    3553.8308            0            0            0    2321.2281 
   292.79017    1203.5248    2334.2308    3537.7557            0            0            0    2334.2308 
    291.5027    1198.2327    2335.2119    3533.4446            0            0            0    2335.2119 
   299.55471    1231.3307    2332.5216    3563.8524            0            0            0    2332.5216 
   293.29613    1205.6046    2295.3263    3500.9309            0            0            0    2295.3263 
   303.13151    1246.0333    2310.0548    3556.0881            0            0            0    2310.0548 
   298.83954     1228.391    2297.3117    3525.7027            0            0            0    2297.3117 
   297.44775      1222.67    2307.2483    3529.9183            0            0            0    2307.2483 
   309.59874    1272.6171    2309.2439     3581.861            0            0            0    2309.2439 
   307.47844    1263.9015     2274.998    3538.8995            0            0            0     2274.998 
Loop time of 11.2235 on 4 procs for 5000 steps with 1380 atoms

Performance: 76.982 ns/day, 0.312 hours/ns, 445.495 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.1444     | 8.5074     | 10.534     |  44.9 | 75.80
Bond    | 0.00017048 | 0.00020672 | 0.00030488 |   0.0 |  0.00
Neigh   | 0.026174   | 0.12108    | 0.26052    |  28.2 |  1.08
Comm    | 0.21788    | 1.8597     | 3.3375     |  81.2 | 16.57
Output  | 0.0008989  | 0.0069895  | 0.021647   |  10.2 |  0.06
Modify  | 0.19418    | 0.7044     | 2.1378     |  98.6 |  6.28
Other   |            | 0.02368    |            |       |  0.21

Nlocal:        345.000 ave         678 max         148 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost:        2854.25 ave        4464 max        1181 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:        19366.8 ave       38533 max        7481 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 77467
Ave neighs/atom = 56.135507
Ave special neighs/atom = 0.0000000
Neighbor list builds = 121
Dangerous builds = 1

# Turn off recentering during production phase
unfix recentering

# Setup trajectory output
dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify     myDump element B W
dump_modify     myDump sort id

# Production (for realistic results, run for 10000000 steps)
reset_timestep  0
run             1000
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.640 | 8.791 | 8.894 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
   307.47844    1263.9015     2274.998    3538.8995            0            0            0     2274.998 
   309.46142    1272.0526    2274.8499    3546.9026            0            0            0    2274.8499 
   300.70977    1236.0787    2301.0588    3537.1374            0            0            0    2301.0588 
   300.53659    1235.3668    2316.1008    3551.4675            0            0            0    2316.1008 
   300.48582    1235.1581    2296.3009     3531.459            0            0            0    2296.3009 
    299.2618    1230.1267    2325.7501    3555.8768            0            0            0    2325.7501 
   303.00905    1245.5299    2321.8238    3567.3537            0            0            0    2321.8238 
   300.07018    1233.4496    2339.2833    3572.7329            0            0            0    2339.2833 
   304.20292    1250.4374    2353.1018    3603.5392            0            0            0    2353.1018 
   304.19487    1250.4043    2334.5087     3584.913            0            0            0    2334.5087 
   294.24283    1209.4961    2335.0535    3544.5496            0            0            0    2335.0535 
Loop time of 2.90512 on 4 procs for 1000 steps with 1380 atoms

Performance: 59.481 ns/day, 0.403 hours/ns, 344.220 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.8627     | 2.2082     | 2.7289     |  22.6 | 76.01
Bond    | 4.042e-05  | 5.3677e-05 | 8.4044e-05 |   0.0 |  0.00
Neigh   | 0.0066184  | 0.030172   | 0.064523   |  13.9 |  1.04
Comm    | 0.05914    | 0.51145    | 0.86887    |  40.7 | 17.61
Output  | 0.0057814  | 0.0073478  | 0.011158   |   2.6 |  0.25
Modify  | 0.0085337  | 0.020869   | 0.042248   |   9.4 |  0.72
Other   |            | 0.127      |            |       |  4.37

Nlocal:        345.000 ave         682 max         147 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost:        2836.25 ave        4427 max        1175 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:        19249.8 ave       38683 max        7433 min
Histogram: 2 0 0 0 1 0 0 0 0 1

Total # of neighbors = 76999
Ave neighs/atom = 55.796377
Ave special neighs/atom = 0.0000000
Neighbor list builds = 23
Dangerous builds = 0


Total wall time: 0:00:14
